Installation

Dependencies

To run metaGOflow you need to make sure you have the following set on your computing environmnet first:

• python [v 3.8+]
• Docker [v 19.+] or Singularity [v 3.7.+]/Apptainer [v 1.+]
• cwltool [v 3.+]
• rocrate [v 0.7.0]
• ruamel.yaml [v 0.17.32+]
• Node.js [v 10.24.0+]
• Available storage ~160GB for databases

Storage while running

Depending on the analysis you are about to run, disk requirements vary. Indicatively, you may have a look at the metaGOflow publication for computing resources used in various cases.

Installation

Get metaGOflow

git clone https://github.com/emo-bon/MetaGOflow
cd MetaGOflow

Download necessary databases (~160GBGB)

You may download the required databases by running the download_dbs.sh script under the Installation folder.

bash Installation/download_dbs.sh -f [Output Directory e.g. ref-dbs] 

If you have one or more already in your system, then create a symbolic link pointing at the ref-dbs folder or at one of its subfolders/files.

The final structure of the DB directory should be like the following:

user@server:~/MetaGOflow: ls ref-dbs/
db_kofam/  diamond/  eggnog/  GO-slim/  interproscan-5.57-90.0/  kegg_pathways/  kofam_ko_desc.tsv  Rfam/  silva_lsu/  silva_ssu/